Zoete Lab members

Postdoctoral researcher CONTACT ME

Research interest 

I am interested in computer-aided drug design and application of machine learning in development of new therapeutic strategies. I am also working on the development of a machine-learning based matching algorithm to study the specificity of TCRs, using rapid structure-based approaches.

Background

• Diploma in Engineering from St Petersburg Chemical-Pharmaceutical Academy
• MSc in Molecular Bioengineering from Technische Universität Dresden
• PhD in Biotechnology and Bioengineering from EPFL, the Swiss Federal Institute of Technology in Lausanne

Master's student CONTACT ME

Research interest

As part of my master’s, I am working to develop a pipeline to create in silico models of T-cell receptors from their sequence, under the supervision of Dr Marta Perez. I especially like the link between biology and computer science. 

Background

I did my Bachelor’s in Biology at the University of Lausanne, where I am currently doing my Master’s in Molecular Life Science with a specialization in bioinformatics. During my studies, I have been active in many committees and associations in the university, such as the Faculty council of Biology and Medicine, the Education committee and the FAE (Fédération des Associations d’étudiants de l’Université de Lausanne).

PhD student CONTACT ME

Research interest 

My current project is to update a database of molecular replacements. The database contains details about the impact on the physico-chemical properties and experimental activities of the molecular modifications, mined from the medicinal chemistry literature. It is meant to support and provide new ideas to researchers in drug discovery, willing to enhance the efficiency of their lead molecules and/or reduce potential side effects. My main PhD project is the creation of CytoxPred, a new in silico predictor of the cytotoxicity of small molecules, for application in the design of new cancer treatments. CytoxPred will be based on existing experimental informations and machine learning predictors.

Background

I obtained my Master’s in Biology at the University of Geneva in 2016, while working as an associate teaching and research assistant. In 2017, for my civil service, I did 6 months’ reforestation within the INESIN, Mexico. On returning, I taught biology in secondary school as a teacher-substitute. I completed my service in 2018 as a project collaborator in the Photovoltaïcs-Laboratory (PV-LAB) at EPFL, the Swiss Federal Institute of Technology in Lausanne. From 2018 to 2019 I did an internship as an assistant writer/editor for SNI Éditions. In 2019, I was an auxiliary research collaborator at HEP, Lausanne and joined the Computer-aided molecular engineering (CAME) and Molecular Modelling Group (MMG) in 2020 as a research collaborator trainee within the UNIL and the SIB Swiss Institute of Bioinformatics. Under Pr Zoete’s supervision, I started my PhD at the University of Lausanne in 2021.

PhD student CONTACT ME

Research

Protein kinases play a major role in cellular activation processes. Consequently, they are important targets for the development of new inhibitors to control the activity of the proteins. In the course of this project, in collaboration with Dr Fanny Krebs, I am developing an approach to study and predict the effects of mutations on the activity of genes from this superfamily.

Background

I hold a Bachelor’s degree in chemical engineering from the Sharif University of Technology. In 2020, I received my Master’s degree in Bioinformatics and Computational biology from the Universities of Bern and Fribourg (joint program). 

PhD student CONTACT ME

Research interest 

Within the the Zoete Lab, we study the diversity of the chemical space occupied by natural compounds with the aim to create a specialized computational workflow for their study. This will accelerate the first in silico evaluation of hard-to-collect molecules as potential modulators of targets of interest in (precision) oncology before their irreversible use in in vivo experiments or the demanding study of their synthetical accessibility. My research interests focus on drug discovery and its joint with multi-omics data analysis. I am excited by how they can be combined through artificial intelligence and computational tools to help patients receive innovative therapies faster. 

Background

I graduated with a Diploma in Pharmacy from the National and Kapodistrian University of Athens in 2021. By joining a group working on pharmacogenetics, I developed my interest in personalized medicine during my undergraduate studies. Parallel to that, I developed my skills in pharmaceutical bioinformatics through online means and complementarily to my studies. After a period of working as a pharmacist, I joined the University of Lausanne in January 2023. 

Postdoctoral researcher CONTACT ME

Research interest 

My research topics focus mainly on the analysis and the development of new molecular modelling and structural bioinformatics tools to help predict the impact of mutations detected in onco-driver proteins.

Background

I undertook my PhD at the University of Strasbourg (France), in collaboration with the Institut de Génétique et de Biologie Moléculaire et Vellulaire (IGBM). This allowed me to gain solid knowledge in organic chemistry and molecular modelling.

PhD student CONTACT ME

Research interest 

My PhD specializes in molecular modelling for cancer immunology and my project consists in developing a novel approach to provide a better understanding and prediction of the specific recognition of pMHC by T-cell receptors, using structure-based rapid approaches.

Background

Before my PhD, I did a Bachelor’s in Biology at the University of the Balearic Islands, followed by a Master’s in Advanced Genetics at the Autonomous University of Barcelona.

Postdoctoral researcher CONTACT ME

Research interest 

I work on the development of a method to describe protein-ligand complexes based on interaction fingerprints. I am also interested in elucidating the molecular features that govern the recognition between T-cell receptors and Major Histocompatibility Complexes.

Background

I hold a Master’s in Biomedical Engineering from the Polytechnic University of Turin, and a PhD in Biotechnology and Bioengineering from EPFL, the Swiss Federal Institute of Technology in Lausanne. I joined the Computer-aided Molecular Engineering group of Pr Vincent Zoete at the University of Lausanne in November 2020.

Master's student CONTACT ME

Research interest 

In the course of my master’s project, I am currently working to develop a novel scoring function approach to predict putative mutation pathogenicity, under the supervision of Dr Fanny Krebs.

Background

I have a Bachelor's in Biology and I am currently doing a Master's in Molecular Science with a specialization in bioinformatics at the University of Lausanne. I recently had the opportunity to publish a review with colleagues in the "Communication biology" section of Nature concerning the involvement of the Nsp1 protein in SARS-CoV-2.

Postdoctoral researcher CONTACT ME

Research interest 

I am working on two different projects, namely (1) the development of a machine-learning bioactivity-prediction model based on chemical similarity, (2) the study of the role of different T-cell receptor residues in the binding to their epitope. I also support and coordinate the Activity-III of the European 3D-Bioinfo Community, in the creation of an automatic pipeline for the design of a ligand-protein benchmarks dataset.

Background

I received my Master’s in Pharmacy from the University of Padova and in 2020, obtained a PhD in Life Sciences from the University of Geneva